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Microorganisms
Volume 11
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Microorganisms, Volume 11, Issue 12 (December 2023) – 187 articles

Cover Story (view full-size image): Cutaneous leishmaniasis (CL) is the most common clinical presentation of leishmaniasis, a Neglected Tropical Disease (NTD). While other presentations of leishmaniasis can be fatal, CL is mostly non-lethal and despite its prevalence not a priority for drug treatment. Yet, CL can be disfiguring and cause prolonged suffering in afflicted individuals. Several drugs are currently used to treat leishmaniasis, although they often have harsh side effects and long treatment regimens, and drug resistance is emerging across the globe. In search of novel drug therapies, researchers have been using biochemical and computational techniques for early-stage drug discovery efforts. This review focuses on the substantial yet fragmented progress in drug discovery for CL and highlights the common challenges for researchers. View this paper
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25 pages, 2993 KiB  
Review
Medically Significant Vector-Borne Viral Diseases in Iran
by Sarah-Jo Paquette, Ayo Yila Simon, Ara XIII, Gary P. Kobinger and Nariman Shahhosseini
Microorganisms 2023, 11(12), 3006; https://doi.org/10.3390/microorganisms11123006 - 18 Dec 2023
Cited by 2 | Viewed by 2915
Abstract
Vector-borne viral diseases (VBVDs) continue to pose a considerable public health risk to animals and humans globally. Vectors have integral roles in autochthonous circulation and dissemination of VBVDs worldwide. The interplay of agricultural activities, population expansion, urbanization, host/pathogen evolution, and climate change, all [...] Read more.
Vector-borne viral diseases (VBVDs) continue to pose a considerable public health risk to animals and humans globally. Vectors have integral roles in autochthonous circulation and dissemination of VBVDs worldwide. The interplay of agricultural activities, population expansion, urbanization, host/pathogen evolution, and climate change, all contribute to the continual flux in shaping the epidemiology of VBVDs. In recent decades, VBVDs, once endemic to particular countries, have expanded into new regions such as Iran and its neighbors, increasing the risk of outbreaks and other public health concerns. Both Iran and its neighboring countries are known to host a number of VBVDs that are endemic to these countries or newly circulating. The proximity of Iran to countries hosting regional diseases, along with increased global socioeconomic activities, e.g., international trade and travel, potentially increases the risk for introduction of new VBVDs into Iran. In this review, we examined the epidemiology of numerous VBVDs circulating in Iran, such as Chikungunya virus, Dengue virus, Sindbis virus, West Nile virus, Crimean–Congo hemorrhagic fever virus, Sandfly-borne phleboviruses, and Hantavirus, in relation to their vectors, specifically mosquitoes, ticks, sandflies, and rodents. In addition, we discussed the interplay of factors, e.g., urbanization and climate change on VBVD dissemination patterns and the consequent public health risks in Iran, highlighting the importance of a One Health approach to further surveil and to evolve mitigation strategies. Full article
(This article belongs to the Section Virology)
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31 pages, 4864 KiB  
Review
Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis
by August Mikucki and Charlene M. Kahler
Microorganisms 2023, 11(12), 3005; https://doi.org/10.3390/microorganisms11123005 - 18 Dec 2023
Viewed by 2165
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These [...] Read more.
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored. Full article
(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease 2.0)
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25 pages, 1473 KiB  
Review
Oral Antibiotics for Bacteremia and Infective Endocarditis: Current Evidence and Future Perspectives
by Gerasimos Eleftheriotis, Markos Marangos, Maria Lagadinou, Sanjay Bhagani and Stelios F. Assimakopoulos
Microorganisms 2023, 11(12), 3004; https://doi.org/10.3390/microorganisms11123004 - 18 Dec 2023
Cited by 1 | Viewed by 4940
Abstract
Bacteremia and endocarditis are two clinical syndromes that, for decades, were managed exclusively with parenteral antimicrobials, irrespective of a given patient’s clinical condition, causative pathogen, or its antibiotic susceptibility profile. This clinical approach, however, was based on low-quality data and outdated expert opinions. [...] Read more.
Bacteremia and endocarditis are two clinical syndromes that, for decades, were managed exclusively with parenteral antimicrobials, irrespective of a given patient’s clinical condition, causative pathogen, or its antibiotic susceptibility profile. This clinical approach, however, was based on low-quality data and outdated expert opinions. When a patient’s condition has improved, gastrointestinal absorption is not compromised, and an oral antibiotic regimen reaching adequate serum concentrations is available, a switch to oral antibacterials can be applied. Although available evidence has reduced the timing of the oral switch in bacteremia to three days/until clinical improvement, there are only scarce data regarding less than 10-day intravenous antibiotic therapy in endocarditis. Many standard or studied oral antimicrobial dosages are smaller than the approved doses for parenteral administration, which is a risk factor for treatment failure; in addition, the gastrointestinal barrier may affect drug bioavailability, especially when the causative pathogen has a minimum inhibitory concentration that is close to the susceptibility breakpoint. A considerable number of patients infected by such near-breakpoint strains may not be potential candidates for oral step-down therapy to non-highly bioavailable antibiotics like beta-lactams; different breakpoints should be determined for this setting. This review will focus on summarizing findings about pathogen-specific tailoring of oral step-down therapy for bacteremia and endocarditis, but will also present laboratory and clinical data about antibiotics such as beta-lactams, linezolid, and fosfomycin that should be studied more in order to elucidate their role and optimal dosage in this context. Full article
(This article belongs to the Special Issue Bacterial Pathogens Associated with Bacteremia)
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14 pages, 7150 KiB  
Article
Comparison and Three-Dimensional Fluorescence Spectrum Analysis of Activated Sludge Treatment with Fenton and UV-Fenton
by Jiamei Wang, Tian Chai and Xin Chen
Microorganisms 2023, 11(12), 3003; https://doi.org/10.3390/microorganisms11123003 - 18 Dec 2023
Viewed by 947
Abstract
This study investigated the effects of single Fenton and Fenton and UV combined processes on the cracking degree of anaerobic sludge under the same conditions. The optimal experimental conditions were obtained by repeated determination of Fe2+ dosage, H2O2 dosage [...] Read more.
This study investigated the effects of single Fenton and Fenton and UV combined processes on the cracking degree of anaerobic sludge under the same conditions. The optimal experimental conditions were obtained by repeated determination of Fe2+ dosage, H2O2 dosage and reaction time, so as to achieve the maximum cracking of sludge. In addition, this study applied three-dimensional fluorescence spectrum analysis technology to analyze the organic matter leached from the treated sludge, and different regions of the three-dimensional fluorescence spectra were analyzed and compared for each treatment condition. Repeated experiments showed that the optimal conditions for Fenton are a pH of 3, reaction time of 40 min, 1.4 g/L of Fe2+ and 9 g/L of H2O2. The Fenton process cracking yielded a protein concentration of 0.66 mg/L and sCOD of 5489 mg/L, and the UV-Fenton pretreatment yielded a protein concentration of 0.74 mg/L and sCOD of 5856 mg/L. The sludge particle size was reduced from the original 54.52 mm to 40.30 mm and 36.37 mm, respectively. In addition to these parameters, it was also demonstrated that the Fenton process has a strong cracking effect on sludge by indicators such as the SEM and sludge water content and that UV irradiation can play a role in assisting and helping sludge cracking. Full article
(This article belongs to the Special Issue Microbial Applications for Sustainable Resource and Energy Recovery)
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11 pages, 4660 KiB  
Communication
Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths
by Adesuwa Sylvia Erhunmwunse, Victor Alonso Guerra, Jung-Chen Liu, Cheryl L. Mackowiak, Ann Rachel Soffes Blount, José Carlos Batista Dubeux, Jr. and Hui-Ling Liao
Microorganisms 2023, 11(12), 3002; https://doi.org/10.3390/microorganisms11123002 - 18 Dec 2023
Cited by 1 | Viewed by 1126
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant–soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing [...] Read more.
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant–soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3–V4 regions. We observed that a well-established RP–bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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15 pages, 5289 KiB  
Article
Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep
by Song Zhong, Jingchun Feng, Jie Kong, Yongji Huang, Xiao Chen and Si Zhang
Microorganisms 2023, 11(12), 3001; https://doi.org/10.3390/microorganisms11123001 - 18 Dec 2023
Cited by 2 | Viewed by 1255
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We [...] Read more.
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics. Full article
(This article belongs to the Special Issue Microbial Communities Involved in the Methane Cycle)
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11 pages, 1387 KiB  
Article
Tigecycline Sensitivity Reduction in Escherichia coli Due to Widely Distributed tet(A) Variants
by Shan Zhang, Mingquan Cui, Dejun Liu, Bo Fu, Tingxuan Shi, Yang Wang, Chengtao Sun and Congming Wu
Microorganisms 2023, 11(12), 3000; https://doi.org/10.3390/microorganisms11123000 - 18 Dec 2023
Viewed by 1352
Abstract
Despite scattered studies that have reported mutations in the tet(A) gene potentially linked to tigecycline resistance in clinical pathogens, the detailed function and epidemiology of these tet(A) variants remains limited. In this study, we analyzed 64 Escherichia coli isolates derived from [...] Read more.
Despite scattered studies that have reported mutations in the tet(A) gene potentially linked to tigecycline resistance in clinical pathogens, the detailed function and epidemiology of these tet(A) variants remains limited. In this study, we analyzed 64 Escherichia coli isolates derived from MacConkey plates supplemented with tigecycline (2 μg/mL) and identified five distinct tet(A) variants that account for reduced sensitivity to tigecycline. In contrast to varied tigecycline MICs (0.25 to 16 μg/mL) of the 64 tet(A)-variant-positive E. coli isolates, gene function analysis confirmed that the five tet(A) variants exhibited a similar capacity to reduce tigecycline sensitivity in DH5α carrying pUC19. Among the observed seven non-synonymous mutations, the V55M mutation was unequivocally validated for its positive role in conferring tigecycline resistance. Interestingly, the variability in tigecycline MICs among the E. coli strains did not correlate with tet(A) gene expression. Instead, a statistically significant reduction in intracellular tigecycline concentrations was noted in strains displaying higher MICs. Genomic analysis of 30 representative E. coli isolates revealed that tet(A) variants predominantly resided on plasmids (n = 14) and circular intermediates (n = 13). Within China, analysis of a well-characterized E. coli collection isolated from pigs and chickens in 2018 revealed the presence of eight tet(A) variants in 103 (4.2%, 95% CI: 3.4–5.0%) isolates across 13 out of 17 tested Chinese provinces or municipalities. Globally, BLASTN analysis identified 21 tet(A) variants in approximately 20.19% (49,423/244,764) of E. coli genomes in the Pathogen Detection database. These mutant tet(A) genes have been widely disseminated among E. coli isolates from humans, food animals, and the environment sectors, exhibiting a growing trend in tet(A) variants over five decades. Our findings underscore the urgency of addressing tigecycline resistance and the underestimated role of tet(A) mutations in this context. Full article
(This article belongs to the Section Veterinary Microbiology)
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18 pages, 1687 KiB  
Systematic Review
The Role of Bifidobacterium in Liver Diseases: A Systematic Review of Next-Generation Sequencing Studies
by Gabriel Henrique Hizo and Pabulo Henrique Rampelotto
Microorganisms 2023, 11(12), 2999; https://doi.org/10.3390/microorganisms11122999 - 17 Dec 2023
Cited by 4 | Viewed by 1621
Abstract
The physiopathology of liver diseases is complex and can be caused by various factors. Bifidobacterium is a bacterial genus commonly found in the human gut microbiome and has been shown to influence the development of different stages of liver diseases significantly. This study [...] Read more.
The physiopathology of liver diseases is complex and can be caused by various factors. Bifidobacterium is a bacterial genus commonly found in the human gut microbiome and has been shown to influence the development of different stages of liver diseases significantly. This study investigated the relationship between the Bifidobacterium genus and liver injury. In this work, we performed a systematic review in major databases using the key terms “Bifidobacterium”, “ALD”, “NAFLD”, “NASH”, “cirrhosis”, and “HCC” to achieve our purpose. In total, 31 articles were selected for analysis. In particular, we focused on studies that used next-generation sequencing (NGS) technologies. The studies focused on assessing Bifidobacterium levels in the diseases and interventional aimed at examining the therapeutic potential of Bifidobacterium in the mentioned conditions. Overall, the abundance of Bifidobacterium was reduced in hepatic pathologies. Low levels of Bifidobacterium were associated with harmful biochemical and physiological parameters, as well as an adverse clinical outcome. However, interventional studies using different drugs and treatments were able to increase the abundance of the genus and improve clinical outcomes. These results strongly support the hypothesis that changes in the abundance of Bifidobacterium significantly influence both the pathophysiology of hepatic diseases and the related clinical outcomes. In addition, our critical assessment of the NGS methods and related statistical analyses employed in each study highlights concerns with the methods used to define the differential abundance of Bifidobacterium, including potential biases and the omission of relevant information. Full article
(This article belongs to the Special Issue Gut Microbiota in Disease, Second Edition)
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19 pages, 14382 KiB  
Article
Temporal Profiling of Host Proteome against Different M. tuberculosis Strains Reveals Delayed Epigenetic Orchestration
by Prabhakar Babele, Mukul K. Midha, Kanury V. S. Rao and Ajay Kumar
Microorganisms 2023, 11(12), 2998; https://doi.org/10.3390/microorganisms11122998 - 16 Dec 2023
Viewed by 1361
Abstract
Apart from being preventable and treatable, tuberculosis is the deadliest bacterial disease afflicting humankind owing to its ability to evade host defence responses, many of which are controlled by epigenetic mechanisms. Here, we report the temporal dynamics of the proteome of macrophage-like host [...] Read more.
Apart from being preventable and treatable, tuberculosis is the deadliest bacterial disease afflicting humankind owing to its ability to evade host defence responses, many of which are controlled by epigenetic mechanisms. Here, we report the temporal dynamics of the proteome of macrophage-like host cells after infecting them for 6, 18, 30, and 42 h with two laboratory strains (H37Ra and H37Rv) and two clinical strains (BND433 and JAL2287) of Mycobacterium tuberculosis (MTB). Using SWATH-MS, the proteins characterized at the onset of infection broadly represented oxidative stress and cell cytoskeleton processes. Intermediary and later stages of infection are accompanied by a reshaping of the combination of proteins implicated in histone stability, gene expression, and protein trafficking. This study provides strain-specific and time-specific variations in the proteome of the host, which might further the development of host-directed therapeutics and diagnostic tools against the pathogen. Also, our findings accentuate the importance of proteomic tools in delineating the complex recalibration of the host defence enabled as an effect of MTB infection. To the best of our knowledge, this is the first comprehensive proteomic account of the host response to avirulent and virulent strains of MTB at different time periods of the life span of macrophage-like cells. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD022352. Full article
(This article belongs to the Special Issue Immunometabolism in Mycobacterium tuberculosis (M.tb) Infection)
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15 pages, 4455 KiB  
Article
Development and Validation of a Highly Sensitive Multiplex Immunoassay for SARS-CoV-2 Humoral Response Monitorization: A Study of the Antibody Response in COVID-19 Patients with Different Clinical Profiles during the First and Second Waves in Cadiz, Spain
by Lucia Olvera-Collantes, Noelia Moares, Ricardo Fernandez-Cisnal, Juan P. Muñoz-Miranda, Pablo Gonzalez-Garcia, Antonio Gabucio, Carolina Freyre-Carrillo, Juan de Dios Jordan-Chaves, Teresa Trujillo-Soto, Maria P. Rodriguez-Martinez, Maria I. Martin-Rubio, Eva Escuer, Manuel Rodriguez-Iglesias, Cecilia Fernandez-Ponce and Francisco Garcia-Cozar
Microorganisms 2023, 11(12), 2997; https://doi.org/10.3390/microorganisms11122997 - 16 Dec 2023
Viewed by 1503
Abstract
There is still a long way ahead regarding the COVID-19 pandemic, since emerging waves remain a daunting challenge to the healthcare system. For this reason, the development of new preventive tools and therapeutic strategies to deal with the disease have been necessary, among [...] Read more.
There is still a long way ahead regarding the COVID-19 pandemic, since emerging waves remain a daunting challenge to the healthcare system. For this reason, the development of new preventive tools and therapeutic strategies to deal with the disease have been necessary, among which serological assays have played a key role in the control of COVID-19 outbreaks and vaccine development. Here, we have developed and evaluated an immunoassay capable of simultaneously detecting multiple IgG antibodies against different SARS-CoV-2 antigens through the use of Bio-PlexTM technology. Additionally, we have analyzed the antibody response in COVID-19 patients with different clinical profiles in Cadiz, Spain. The multiplex immunoassay presented is a high-throughput and robust immune response monitoring tool capable of concurrently detecting anti-S1, anti-NC and anti-RBD IgG antibodies in serum with a very high sensitivity (94.34–97.96%) and specificity (91.84–100%). Therefore, the immunoassay proposed herein may be a useful monitoring tool for individual humoral immunity against SARS-CoV-2, as well as for epidemiological surveillance. In addition, we show the values of antibodies against multiple SARS-CoV-2 antigens and their correlation with the different clinical profiles of unvaccinated COVID-19 patients in Cadiz, Spain, during the first and second waves of the pandemic. Full article
(This article belongs to the Special Issue Coronaviruses: Past, Present, and Future)
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17 pages, 1763 KiB  
Review
Rocahepevirus ratti as an Emerging Cause of Acute Hepatitis Worldwide
by Sara Benavent, Silvia Carlos and Gabriel Reina
Microorganisms 2023, 11(12), 2996; https://doi.org/10.3390/microorganisms11122996 - 16 Dec 2023
Cited by 7 | Viewed by 2178
Abstract
The hepatitis E virus (HEV) is a widespread human infection that causes mainly acute infection and can evolve to a chronic manifestation in immunocompromised individuals. In addition to the common strains of hepatitis E virus (HEV-A), known as Paslahepevirus balayani, pathogenic to [...] Read more.
The hepatitis E virus (HEV) is a widespread human infection that causes mainly acute infection and can evolve to a chronic manifestation in immunocompromised individuals. In addition to the common strains of hepatitis E virus (HEV-A), known as Paslahepevirus balayani, pathogenic to humans, a genetically highly divergent rat origin hepevirus (RHEV) can cause hepatitis possessing a potential risk of cross-species infection and zoonotic transmission. Rocahepevirus ratti, formerly known as Orthohepevirus C, is a single-stranded RNA virus, recently reassigned to Rocahepevirus genus in the Hepeviridae family, including genotypes C1 and C2. RHEV primarily infects rats but has been identified as a rodent zoonotic virus capable of infecting humans through the consumption of contaminated food or water, causing both acute and chronic hepatitis cases in both animals and humans. This review compiles data concluding that 60% (295/489) of RHEV infections are found in Asia, being the continent with the highest zoonotic and transmission potential. Asia not only has the most animal cases but also 16 out of 21 human infections worldwide. Europe follows with 26% (128/489) of RHEV infections in animals, resulting in four human cases out of twenty-one globally. Phylogenetic analysis and genomic sequencing will be employed to gather global data, determine epidemiology, and assess geographical distribution. This information will enhance diagnostic accuracy, pathogenesis understanding, and help prevent cross-species transmission, particularly to humans. Full article
(This article belongs to the Special Issue Emerging Pathogens Causing Acute Hepatitis)
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8 pages, 1323 KiB  
Case Report
A Large-Scale Outbreak of Trichinellosis from Infected Wild Boar Meat in Croatia and the Role of Real-Time PCR Assays in Confirming the Source of the Disease
by Davor Balić, Tomislav Dijanić, Marija Agičić, Josip Barić, Maria Kaltenbrunner, Hrvoje Krajina, Rupert Hochegger, Mario Škrivanko and Karlo Kožul
Microorganisms 2023, 11(12), 2995; https://doi.org/10.3390/microorganisms11122995 - 16 Dec 2023
Cited by 2 | Viewed by 1260
Abstract
Background: Trichinellosis in Croatia posed a significant health concern during the 1990s, followed by a notable improvement in the epidemiological situation. However, in 2017, there was a resurgence, with 37 recorded cases in 3 outbreaks and 3 sporadic cases. The source of this [...] Read more.
Background: Trichinellosis in Croatia posed a significant health concern during the 1990s, followed by a notable improvement in the epidemiological situation. However, in 2017, there was a resurgence, with 37 recorded cases in 3 outbreaks and 3 sporadic cases. The source of this epidemic was homemade meat products derived from wild boar meat, leading to 26 infections. Methods: At the beginning of the outbreak and during the treatment of the patients, the medical and epidemiological records prepared throughout the investigation and over the course of patient treatment were reviewed. The recovery of the first-stage (L1) larvae from suspect meat products was achieved by artificial digestion. The molecular identification of the isolated larvae was performed by multiplex PCR. The molecular identification of the meat used to prepare the meat products was performed by real-time PCR assays. Results: The epidemic started in early 2017. In total, 71 exposed persons were documented: 26 with clinical symptoms and 3 hospitalised in two cities in different counties. The L1 burden in three different meat products was from 5.25 to 7.08 larvae per gram (LPG), and T. spiralis was determined as the aetiological agent of the outbreak. The molecular and biological identification confirmed that implicated meat products were made solely from wild boar meat. Conclusions: Although trichinellosis is no longer a frequent occurrence in Croatia, several cases are still registered nearly every year. Wild boar meat poses an important risk factor for human health if compulsory testing is not conducted before consumption, especially if the meat products are consumed without proper thermal processing. Full article
(This article belongs to the Special Issue Detection and Epidemiology of Vector-, Food- and Water-Borne Pathogens with a Focus on One Health Approaches)
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20 pages, 4732 KiB  
Article
Microbial Diversity and Community Structure of Wastewater-Driven Microalgal Biofilms
by Olga Blifernez-Klassen, Julia Hassa, Diana L. Reinecke, Tobias Busche, Viktor Klassen and Olaf Kruse
Microorganisms 2023, 11(12), 2994; https://doi.org/10.3390/microorganisms11122994 - 16 Dec 2023
Cited by 1 | Viewed by 1802
Abstract
Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and [...] Read more.
Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and 16S rRNA gene amplicon sequencing, we profiled the microbial communities of four microbial biofilms from ATS systems operated with municipal wastewater (mWW), diluted cattle and pig manure (CattleM and PigM), and biogas plant effluent supernatant (BGE) in comparison to the initial inocula and the respective wastewater substrates. The wastewater-driven biofilms differed significantly in their biodiversity and structure, exhibiting an inocula-independent but substrate-dependent establishment of the microbial communities. The prokaryotic communities were comparable among themselves and with other microbiomes of aquatic environments and were dominated by metabolically flexible prokaryotes such as nitrifiers, polyphosphate-accumulating and algicide-producing microorganisms, and anoxygenic photoautotrophs. Striking differences occurred in eukaryotic communities: While the mWW biofilm was characterized by high biodiversity and many filamentous (benthic) microalgae, the agricultural wastewater-fed biofilms consisted of less diverse communities with few benthic taxa mainly inhabited by unicellular chlorophytes and saprophytes/parasites. This study advances our understanding of the microbiome structure and function within the ATS-based wastewater treatment process. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Water and Wastewater Treatment)
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14 pages, 1101 KiB  
Article
Enterotoxigenic and Antimicrobic Susceptibility Profile of Staphylococcus aureus Isolates from Fresh Cheese in Croatia
by Ivana Ljevaković-Musladin, Lidija Kozačinski, Marija Krilanović, Marina Vodnica Martucci, Mato Lakić, Luca Grispoldi and Beniamino T. Cenci-Goga
Microorganisms 2023, 11(12), 2993; https://doi.org/10.3390/microorganisms11122993 - 15 Dec 2023
Viewed by 1078
Abstract
Certain Staphylococcus aureus strains harbour staphylococcal enterotoxin genes and hence can produce enterotoxin during their growth in food. Therefore, food can be a source of staphylococcal food poisoning, one of the most common food-borne diseases worldwide. Epidemiological data show that S. aureus is [...] Read more.
Certain Staphylococcus aureus strains harbour staphylococcal enterotoxin genes and hence can produce enterotoxin during their growth in food. Therefore, food can be a source of staphylococcal food poisoning, one of the most common food-borne diseases worldwide. Epidemiological data show that S. aureus is often present in raw milk cheeses, and consequently, cheeses are often the source of staphylococcal food poisoning outbreaks. The aim of this study was to determine the phenotypic characteristics of S. aureus isolates from fresh cheese, including antibiotic susceptibility; the presence of classical sea-see enterotoxin genes through molecular methods; and the isolate’s ability to produce SEA-SEE enterotoxins in vitro through reversed passive latex agglutination. A total of 180 coagulase-positive staphylococci were isolated from 18 out of 30 cheese samples, and 175 were confirmed as S. aureus through latex agglutination and API STAPH tests. All isolates possessed phenotypic characteristics typical for S. aureus, with certain variations in the egg yolk reaction (18.3% of the isolates showed a weak reaction and 28% no reaction at all) and haemolysis pattern (36.6% of the isolates produced double-haemolysis and 4.6% were non-haemolytic). Antibiotic resistance was observed in 1.1% of the isolates and to mupirocin only. Real-time PCR detected the sec gene in 34 (19.4%) isolates, but most isolates (80.6%) were not enterotoxigenic. For all 34 (19.4%) strains that carried the sec gene, the RPLA method detected the production of the SEC enterotoxin in vitro. For those enterotoxigenic strains, the possibility of enterotoxin production in fresh cheese could not be ruled out. Full article
(This article belongs to the Special Issue Microorganisms and Fermented Foods 2.0)
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11 pages, 317 KiB  
Article
The Presence of Legionella in Water Used for Car Washing: Implications for Public Health
by Pasqualina Laganà, Alessio Facciolà, Roberta Palermo, Osvalda De Giglio, Santi Antonino Delia and Maria Eufemia Gioffrè
Microorganisms 2023, 11(12), 2992; https://doi.org/10.3390/microorganisms11122992 - 15 Dec 2023
Viewed by 1283
Abstract
Although today all of the aspects of Legionella are better understood than in the past, in many countries the interest is still mainly focused on healthcare and tourism facilities. Other at-risk areas are less explored, such as those where workers are often in [...] Read more.
Although today all of the aspects of Legionella are better understood than in the past, in many countries the interest is still mainly focused on healthcare and tourism facilities. Other at-risk areas are less explored, such as those where workers are often in contact with water during their activities. In reality, any water system capable of producing aerosols can be considered a potential source of Legionella transmission, including car washes, where a large number of users work and flow through annually. From January to May 2022, 120 samples were carried out in 30 car washes located in Messina (Italy): 60 samples of water and 60 of aerosols. The aim of this investigation was to evaluate the risk of legionellosis in car washing workers exposed to potentially contaminated aerosols. To increase the probability of finding Legionella, the sample collections were organized on different days of the week. Of the total samples taken, 10 (8.3%) were positive for Legionella: seven (11.7%) water (range 100–1000 CFU) and three (5%) aerosol (range 10–150 CFU) samples. Detected serogroups were L. pneumophila sgr 1, 7, 10 and Legionella gormanii. Given the results obtained, preventative measures should be implemented in such facilities in order to protect the health of users and car wash operators. Full article
(This article belongs to the Special Issue Clinical and Environmental Surveillance for the Prevention of Legionellosis)
14 pages, 312 KiB  
Article
Antimicrobial Resistance Profiles of Enterococcus faecium and Enterococcus faecalis Isolated from Healthy Dogs and Cats in South Korea
by Bo-Youn Moon, Md. Sekendar Ali, Ji-Hyun Choi, Ye-Eun Heo, Yeon-Hee Lee, Hee-Seung Kang, Tae-Sun Kim, Soon-Seek Yoon, Dong-Chan Moon and Suk-Kyung Lim
Microorganisms 2023, 11(12), 2991; https://doi.org/10.3390/microorganisms11122991 - 15 Dec 2023
Cited by 1 | Viewed by 1981
Abstract
Enterococcus spp. are typically found in the gastrointestinal tracts of humans and animals. However, they have the potential to produce opportunistic infections that can be transmitted to humans or other animals, along with acquired antibiotic resistance. In this study, we aimed to investigate [...] Read more.
Enterococcus spp. are typically found in the gastrointestinal tracts of humans and animals. However, they have the potential to produce opportunistic infections that can be transmitted to humans or other animals, along with acquired antibiotic resistance. In this study, we aimed to investigate the antimicrobial resistance profiles of Enterococcus faecium and Enterococcus faecalis isolates obtained from companion animal dogs and cats in Korea during 2020–2022. The resistance rates in E. faecalis towards most of the tested antimicrobials were relatively higher than those in E. faecium isolated from dogs and cats. We found relatively higher resistance rates to tetracycline (65.2% vs. 75.2%) and erythromycin (39.5% vs. 49.6%) in E. faecalis isolated from cats compared to those from dogs. However, in E. faecium, the resistance rates towards tetracycline (35.6% vs. 31.5%) and erythromycin (40.3% vs. 35.2%) were comparatively higher for dog isolates than cats. No or very few E. faecium and E. faecalis isolates were found to be resistant to daptomycin, florfenicol, tigecycline, and quinupristin/dalfopristin. Multidrug resistance (MDR) was higher in E. faecalis recovered from cats (44%) and dogs (33.9%) than in E. faecium isolated from cats (24.1%) and dogs (20.5%). Moreover, MDR patterns in E. faecalis isolates from dogs (27.2%) and cats (35.2%) were shown to encompass five or more antimicrobials. However, E. faecium isolates from dogs (at 13.4%) and cats (at 14.8%) were resistant to five or more antimicrobials. Taken together, the prevalence of antimicrobial-resistant enterococci in companion animals presents a potential public health concern. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
23 pages, 1834 KiB  
Review
One Health Perspectives on Food Safety in Minimally Processed Vegetables and Fruits: From Farm to Fork
by Maria Isabel Santos, Madalena Grácio, Mariana Camoesas Silva, Laurentina Pedroso and Ana Lima
Microorganisms 2023, 11(12), 2990; https://doi.org/10.3390/microorganisms11122990 - 15 Dec 2023
Cited by 7 | Viewed by 3903
Abstract
While food markets and food production chains are experiencing exponential growth, global attention to food safety is steadily increasing. This is particularly crucial for ready-to-eat products such as fresh-cut salads and fruits, as these items are consumed raw without prior heat treatment, making [...] Read more.
While food markets and food production chains are experiencing exponential growth, global attention to food safety is steadily increasing. This is particularly crucial for ready-to-eat products such as fresh-cut salads and fruits, as these items are consumed raw without prior heat treatment, making the presence of pathogenic microorganisms quite frequent. Moreover, many studies on foodborne illnesses associated with these foods often overlook the transmission links from the initial contamination source. The prevention and control of the dissemination of foodborne pathogens should be approached holistically, involving agricultural production, processing, transport, food production, and extending to final consumption, all while adopting a One Health perspective. In this context, our objective is to compile available information on the challenges related to microbiological contamination in minimally handled fruits and vegetables. This includes major reported outbreaks, specific bacterial strains, and associated statistics throughout the production chain. We address the sources of contamination at each stage, along with issues related to food manipulation and disinfection. Additionally, we provide potential solutions to promote a healthier approach to fresh-cut fruits and vegetables. This information will be valuable for both researchers and food producers, particularly those focused on ensuring food safety and quality. Full article
(This article belongs to the Topic Food Hygiene and Food Safety)
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12 pages, 16466 KiB  
Article
Association between the Presence of Resistance Genes and Sanitiser Resistance of Listeria monocytogenes Isolates Recovered from Different Food-Processing Facilities
by Yue Cheng, Zeinabossadat Ebrahimzadeh Mousavi, Vincenzo Pennone, Daniel Hurley and Francis Butler
Microorganisms 2023, 11(12), 2989; https://doi.org/10.3390/microorganisms11122989 - 15 Dec 2023
Cited by 1 | Viewed by 1225
Abstract
Sanitisers are widely used in cleaning food-processing facilities, but their continued use may cause an increased resistance of pathogenic bacteria. Several genes have been attributed to the increased sanitiser resistance ability of L. monocytogenes. This study determined the presence of sanitiser resistance [...] Read more.
Sanitisers are widely used in cleaning food-processing facilities, but their continued use may cause an increased resistance of pathogenic bacteria. Several genes have been attributed to the increased sanitiser resistance ability of L. monocytogenes. This study determined the presence of sanitiser resistance genes in Irish-sourced L. monocytogenes isolates and explored the association with phenotypic sanitiser resistance. The presence of three genes associated with sanitiser resistance and a three-gene cassette (mdrL, qacH, emrE, bcrABC) were determined in 150 L. monocytogenes isolates collected from Irish food-processing facilities. A total of 23 isolates contained bcrABC, 42 isolates contained qacH, one isolate contained emrE, and all isolates contained mdrL. Additionally, 47 isolates were selected and grouped according to the number and type of resistance genes, and the minimal inhibitory concentration (MIC) of these isolates for benzalkonium chloride (BAC) was determined experimentally using the broth microdilution method. The BAC resistance of the strain carrying the bcrABC gene cassette was significantly higher than that of strains lacking the gene cassette, and the BAC resistance of the strain carrying the qacH gene was significantly higher than that of strains lacking the qacH gene (p < 0.05). Isolates harbouring both the qacH and bcrABC genes did not show higher BAC resistance. With respect to environmental factors, there was no significant difference in MIC values for isolates recovered from different processing facilities. In summary, this investigation highlights the prevalence of specific sanitiser resistance genes in L. monocytogenes isolates from Irish food-processing settings. While certain genes correlated with increased resistance to benzalkonium chloride, the combination of multiple genes did not necessarily amplify this resistance. Full article
(This article belongs to the Special Issue An Update on Listeria monocytogenes 2.0)
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16 pages, 4860 KiB  
Article
Isolation and Evaluation of Streptomyces melanogenes YBS22 with Potential Application for Biocontrol of Rice Blast Disease
by Luyang Song, Fei Wang, Chuang Liu, Zhengzhe Guan, Mengjiao Wang, Rongrong Zhong, Huijun Xi, Ying Zhao and Caiyi Wen
Microorganisms 2023, 11(12), 2988; https://doi.org/10.3390/microorganisms11122988 - 15 Dec 2023
Cited by 1 | Viewed by 1367
Abstract
Plant diseases caused by pathogenic fungi pose a significant threat to agricultural production. This study reports on a strain YBS22 with broad-spectrum antifungal activity that was isolated and identified, and its active metabolites were purified and systematically studied. Based on a whole genome [...] Read more.
Plant diseases caused by pathogenic fungi pose a significant threat to agricultural production. This study reports on a strain YBS22 with broad-spectrum antifungal activity that was isolated and identified, and its active metabolites were purified and systematically studied. Based on a whole genome sequence analysis, the new strain YBS22 was identified as Streptomyces melanogenes. Furthermore, eight gene clusters were predicted in YBS22 that are responsible for the synthesis of bioactive secondary metabolites. These clusters have homologous sequences in the MIBiG database with a similarity of 100%. The antifungal effects of YBS22 and its crude extract were evaluated in vivo and vitro. Our findings revealed that treatment with the strain YBS22 and its crude extract significantly reduced the size of necrotic lesions caused by Magnaporthe oryzae on rice leaves. Further analysis led to the isolation and purification of an active compound from the crude extract of the strain YBS22, identified as N-formylantimycin acid methyl ester, an analog of antimycin, characterized by NMR and MS analyses. Consistently, the active compound can significantly inhibit the germination and development of M. oryzae spores in a manner that is both dose- and time-dependent. As a result, we propose that the strain YBS22 could serve as a novel source for the development of biological agents aimed at controlling rice blast disease. Full article
(This article belongs to the Section Plant Microbe Interactions)
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22 pages, 929 KiB  
Review
State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs
by Mikhail A. Kulyashov, Semyon K. Kolmykov, Tamara M. Khlebodarova and Ilya R. Akberdin
Microorganisms 2023, 11(12), 2987; https://doi.org/10.3390/microorganisms11122987 - 14 Dec 2023
Cited by 2 | Viewed by 1846
Abstract
Methanotrophy is the ability of an organism to capture and utilize the greenhouse gas, methane, as a source of energy-rich carbon. Over the years, significant progress has been made in understanding of mechanisms for methane utilization, mostly in bacterial systems, including the key [...] Read more.
Methanotrophy is the ability of an organism to capture and utilize the greenhouse gas, methane, as a source of energy-rich carbon. Over the years, significant progress has been made in understanding of mechanisms for methane utilization, mostly in bacterial systems, including the key metabolic pathways, regulation and the impact of various factors (iron, copper, calcium, lanthanum, and tungsten) on cell growth and methane bioconversion. The implementation of -omics approaches provided vast amount of heterogeneous data that require the adaptation or development of computational tools for a system-wide interrogative analysis of methanotrophy. The genome-scale mathematical modeling of its metabolism has been envisioned as one of the most productive strategies for the integration of muti-scale data to better understand methane metabolism and enable its biotechnological implementation. Herein, we provide an overview of various computational strategies implemented for methanotrophic systems. We highlight functional capabilities as well as limitations of the most popular web resources for the reconstruction, modification and optimization of the genome-scale metabolic models for methane-utilizing bacteria. Full article
(This article belongs to the Special Issue Editorial Board Members' Collection Series: Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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13 pages, 1798 KiB  
Article
The Genomic Characteristics of an Arthritis-Causing Salmonella pullorum
by Zhiyuan Lu, Jiaqi Huang, Peiyong Li, Mengze Song, Ben Liu, Wenli Tang and Shuhong Sun
Microorganisms 2023, 11(12), 2986; https://doi.org/10.3390/microorganisms11122986 - 14 Dec 2023
Cited by 2 | Viewed by 1304
Abstract
Salmonella enterica subsp. enterica serovar Gallinarum biovar pullorum (Salmonella pullorum) is an avian-specific pathogen that has caused considerable economic losses to the poultry industry. High endemicity, poor implementation of hygiene measures, and lack of effective vaccines hinder the prevention and control of [...] Read more.
Salmonella enterica subsp. enterica serovar Gallinarum biovar pullorum (Salmonella pullorum) is an avian-specific pathogen that has caused considerable economic losses to the poultry industry. High endemicity, poor implementation of hygiene measures, and lack of effective vaccines hinder the prevention and control of this disease in intensively maintained poultry flocks. In recent years, the incidence of arthritis in chicks caused by Salmonella pullorum infection has increased. In this study, four Salmonella pullorum strains were identified from the livers, spleens, and joint fluids of Qingjiaoma chicken breeders with arthritis clinical signs, and an arthritis model of chicks was successfully established using SP206-2. Whole genome sequencing of the SP206-2 strain showed that the genome was 4,730,579 bp, 52.16% GC content, and contained 5007 genes, including 4729 protein-coding regions. The genomic analysis of four arthritis-causing isolates and three diarrhea-causing isolates showed that the genome of arthritis-causing isolates was subject to nonsynonymous mutations, shift mutations, and gene copy deletions. An SNP phylogenetic tree analysis showed that arthritis-causing isolates are located in a different evolutionary branch from diarrhea-causing isolates. Further differential genes analysis showed that the genome of arthritis-causing isolates had missense mutations in genes related to substance metabolism and substance transport, as a result of adaptive evolution. Full article
(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases)
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21 pages, 2033 KiB  
Review
AAV Immunotoxicity: Implications in Anti-HBV Gene Therapy
by Ridhwaanah Jacobs, Makafui Dennis Dogbey, Njabulo Mnyandu, Keila Neves, Stefan Barth, Patrick Arbuthnot and Mohube Betty Maepa
Microorganisms 2023, 11(12), 2985; https://doi.org/10.3390/microorganisms11122985 - 14 Dec 2023
Cited by 1 | Viewed by 1946
Abstract
Hepatitis B virus (HBV) has afflicted humankind for decades and there is still no treatment that can clear the infection. The development of recombinant adeno-associated virus (rAAV)-based gene therapy for HBV infection has become important in recent years and research has made exciting [...] Read more.
Hepatitis B virus (HBV) has afflicted humankind for decades and there is still no treatment that can clear the infection. The development of recombinant adeno-associated virus (rAAV)-based gene therapy for HBV infection has become important in recent years and research has made exciting leaps. Initial studies, mainly using mouse models, showed that rAAVs are non-toxic and induce minimal immune responses. However, several later studies demonstrated rAAV toxicity, which is inextricably associated with immunogenicity. This is a major setback for the progression of rAAV-based therapies toward clinical application. Research aimed at understanding the mechanisms behind rAAV immunity and toxicity has contributed significantly to the inception of approaches to overcoming these challenges. The target tissue, the features of the vector, and the vector dose are some of the determinants of AAV toxicity, with the latter being associated with the most severe adverse events. This review discusses our current understanding of rAAV immunogenicity, toxicity, and approaches to overcoming these hurdles. How this information and current knowledge about HBV biology and immunity can be harnessed in the efforts to design safe and effective anti-HBV rAAVs is discussed. Full article
(This article belongs to the Special Issue Adeno-Associated Virus Biology and AAV Vector-Mediated Gene Therapy)
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12 pages, 1865 KiB  
Article
Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants
by Katherine V. Weigh, Bruna D. Batista, Huong Hoang and Paul G. Dennis
Microorganisms 2023, 11(12), 2984; https://doi.org/10.3390/microorganisms11122984 - 14 Dec 2023
Cited by 1 | Viewed by 1497
Abstract
The ability to sense and direct movement along chemical gradients is known as ‘chemotaxis’ and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change [...] Read more.
The ability to sense and direct movement along chemical gradients is known as ‘chemotaxis’ and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress. Full article
(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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33 pages, 23892 KiB  
Article
Bacillus subtilis 26D Triggers Induced Systemic Resistance against Rhopalosiphum padi L. by Regulating the Expression of Genes AGO, DCL and microRNA in Bread Spring Wheat
by Sergey D. Rumyantsev, Svetlana V. Veselova, Guzel F. Burkhanova, Valentin Y. Alekseev and Igor V. Maksimov
Microorganisms 2023, 11(12), 2983; https://doi.org/10.3390/microorganisms11122983 - 14 Dec 2023
Cited by 3 | Viewed by 1804
Abstract
Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is [...] Read more.
Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is a serious pest that causes significant damage to crops throughout the world. However, the function of plant miRNAs in the response to aphid infestation remains unclear. The results of this work showed that B. subtilis 26D stimulated aphid resistance in wheat plants, inducing the expression of genes of hormonal signaling pathways ICS, WRKY13, PR1, ACS, EIN3, PR3, and ABI5. In addition, B. subtilis 26D activated the RNAi mechanism and regulated the expression of nine conserved miRNAs through activation of the ethylene, salicylic acid (SA), and abscisic acid (ABA) signaling pathways, which was demonstrated by using treatments with phytohormones. Treatment of plants with SA, ethylene, and ABA acted in a similar manner to B. subtilis 26D on induction of the expression of the AGO4, AGO5 and DCL2, DCL4 genes, as well as the expression of nine conserved miRNAs. Different patterns of miRNA expression were found in aphid-infested plants and in plants treated with B. subtilis 26D or SA, ethylene, and ABA and infested by aphids, suggesting that miRNAs play multiple roles in the plant response to phloem-feeding insects, associated with effects on hormonal signaling pathways, redox metabolism, and the synthesis of secondary metabolites. Our study provides new data to further elucidate the fine mechanisms of bacterial-induced priming. However, further extensive work is needed to fully unravel these mechanisms. Full article
(This article belongs to the Special Issue Advances in Microbial and Plant Biotechnology)
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21 pages, 5128 KiB  
Article
Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome
by Catrione Lee, Rahat Zaheer, Krysty Munns, Devin B. Holman, Gary Van Domselaar, Athanasios Zovoilis and Tim A. McAllister
Microorganisms 2023, 11(12), 2982; https://doi.org/10.3390/microorganisms11122982 - 14 Dec 2023
Cited by 1 | Viewed by 1695
Abstract
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of “natural” feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to [...] Read more.
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of “natural” feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems. Full article
(This article belongs to the Section Veterinary Microbiology)
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10 pages, 1935 KiB  
Article
Diversity of Fecal Indicator Enterococci among Different Hosts: Importance to Water Contamination Source Tracking
by Soichiro Tamai and Yoshihiro Suzuki
Microorganisms 2023, 11(12), 2981; https://doi.org/10.3390/microorganisms11122981 - 14 Dec 2023
Cited by 7 | Viewed by 1420
Abstract
Enterococcus spp. are common bacteria present in the intestinal tracts of animals and are used as fecal indicators in aquatic environments. On the other hand, enterococci are also known as opportunistic pathogens. Elucidating their composition in the intestinal tracts of domestic animals can [...] Read more.
Enterococcus spp. are common bacteria present in the intestinal tracts of animals and are used as fecal indicators in aquatic environments. On the other hand, enterococci are also known as opportunistic pathogens. Elucidating their composition in the intestinal tracts of domestic animals can assist in estimating the sources of fecal contamination in aquatic environments. However, information on the species and composition of enterococci in animal hosts (except humans) is still lacking. In this study, enterococci were isolated from the feces of cattle, pigs, birds, and humans using selective media. Enterococcal species were identified using mass spectrometry technology, and each host was characterized by diversity and cluster analysis. The most dominant species were E. hirae in cattle, E. faecium in birds, and E. faecalis in pigs and humans. Cattle had the highest alpha diversity, with high interindividual and livestock farm diversity. The dominant enterococcal species in pigs and humans were identical, and cluster analysis showed that the majority of the two hosts’ species clustered together. Full article
(This article belongs to the Special Issue Water Microorganisms Associated with Human Health)
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15 pages, 821 KiB  
Article
Satureja hortensis L. and Calendula officinalis L., Two Romanian Plants, with In Vivo Antiparasitic Potential against Digestive Parasites of Swine
by Mihai-Horia Băieş, Vlad-Dan Cotuţiu, Marina Spînu, Attila Mathe, Anamaria Cozma-Petruț, Vlad I. Bocǎneţ and Vasile Cozma
Microorganisms 2023, 11(12), 2980; https://doi.org/10.3390/microorganisms11122980 - 13 Dec 2023
Viewed by 1401
Abstract
Internal parasitic diseases of swine constitute a major welfare and health concern in low-input livestock farming. Due to an increase in chemical resistance, phytotherapeutic remedies have become an alternative for the prophylaxis and therapy of digestive parasitosis, albeit few remedies have been subjected [...] Read more.
Internal parasitic diseases of swine constitute a major welfare and health concern in low-input livestock farming. Due to an increase in chemical resistance, phytotherapeutic remedies have become an alternative for the prophylaxis and therapy of digestive parasitosis, albeit few remedies have been subjected to scientific validation. Low-input swine farming in Romania has adopted the traditional use of phytotherapy for controlling pathogens in livestock. The current study aimed to assess the antiparasitic potential of Calendula officinalis and Satureja hortensis against digestive parasites of swine in two low-input farms. The fecal samples were collected from sows, fatteners, and weaners, and were tested using the following coproparasitological methods: centrifugal sedimentation, flotation (Willis, McMaster egg counting technique), Ziehl–Neelsen stain modified by Henricksen, modified Blagg method, and in vitro nematode larvae/protozoan oocyst cultures. Six species of digestive parasites were diagnosed, namely Ascaris suum, Trichuris suis, Oesophagostomum spp., Balantioides coli, Eimeria spp., and Cryptosporidium spp., in various combinations, dependent on the swine category. A dose of 140 mg/kg bw/day of C. officinalis and 100 mg/kg bw/day of S. hortensis powders administered for 10 consecutive days revealed a strong antiprotozoal and anthelmintic activity on the aforementioned parasites. The curative efficacy can be attributed to the presence of polyphenols, sterols, tocopherols, and methoxylated flavones. In conclusion, our results indicate that S. hortensis and C. officinalis are promising alternatives to the commercially available antiparasitics, enabling their use as natural antiparasitic products against gastrointestinal parasites in pigs. Full article
(This article belongs to the Special Issue Parasitic Diseases in Livestock)
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14 pages, 3560 KiB  
Article
Biodegradation of Cholesterol by Enterococcus faecium YY01
by Ruimin Yang, Shahbaz Ahmad, Hongyan Liu, Qianqian Xu, Chunhua Yin, Yang Liu, Haiyang Zhang and Hai Yan
Microorganisms 2023, 11(12), 2979; https://doi.org/10.3390/microorganisms11122979 - 13 Dec 2023
Viewed by 1217
Abstract
Cholesterol (CHOL) is one of the risk factors causing the blockage of the arterial wall, atherosclerosis, coronary heart disease, and other serious cardiovascular diseases. Here, a promising bacterial strain for biodegrading CHOL was successfully isolated from the gut of healthy individuals and identified [...] Read more.
Cholesterol (CHOL) is one of the risk factors causing the blockage of the arterial wall, atherosclerosis, coronary heart disease, and other serious cardiovascular diseases. Here, a promising bacterial strain for biodegrading CHOL was successfully isolated from the gut of healthy individuals and identified as Enterococcus faecium YY01 with an analysis of the 16S rDNA sequence. An initial CHOL of 1.0 g/L was reduced to 0.5 g/L in 5 days, and glucose and beef extract were found to be optimal carbon and nitrogen sources for the rapid growth of YY01, respectively. To gain further insight into the mechanisms underlying CHOL biodegradation, the draft genome of YY01 was sequenced using Illumina HiSeq. Choloylglycine hydrolase, acyltransferase, and alkyl sulfatase was encoded by gene0586, gene1890, and gene2442, which play crucial roles in converting 3α, 7α, 12α-trihydroxy-5β-choranic acid to choline-CoA and then choline-CoA to bile acid. Notably, choloylglycine hydrolase was closely related to the biosynthesis of both primary and secondary bile acid. The findings of this study provide valuable insights into the metabolism pathway of CHOL biodegradation by YY01 and offer a potential avenue for the development of bacterioactive drugs against hypercholesterolemia. Full article
(This article belongs to the Section Microbial Biotechnology)
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29 pages, 5077 KiB  
Article
Nutrient and Microbiome-Mediated Plant–Soil Feedback in Domesticated and Wild Andropogoneae: Implications for Agroecosystems
by Amanda Quattrone, Yuguo Yang, Pooja Yadav, Karrie A. Weber and Sabrina E. Russo
Microorganisms 2023, 11(12), 2978; https://doi.org/10.3390/microorganisms11122978 - 13 Dec 2023
Viewed by 1513
Abstract
Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF [...] Read more.
Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73-wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative PSF based on growth, phenotypic traits, and foliar nutrient concentrations for maize B73-wt, which grew slower in maize-conditioned soil than prairie grass-conditioned soil. In contrast, teosinte and A. gerardii showed few consistent feedback responses. Both rhizobiome and nutrient-mediated mechanisms were implicated in PSF. Based on 16S rRNA gene amplicon sequencing, the rhizosphere bacterial community composition differed significantly after conditioning by prairie grass and maize plants, and the final soil nutrients were significantly influenced by conditioning, more so than by the feedback plants. These results suggest PSF-mediated soil domestication in agricultural settings can develop quickly and reduce crop productivity mediated by PSF involving changes to both the soil rhizobiomes and nutrient availability. Full article
(This article belongs to the Special Issue Rhizosphere Microbial Community 2.0)
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18 pages, 3225 KiB  
Article
HLA-DQ2/8 and COVID-19 in Celiac Disease: Boon or Bane
by Aaron Lerner, Carina Benzvi and Aristo Vojdani
Microorganisms 2023, 11(12), 2977; https://doi.org/10.3390/microorganisms11122977 - 13 Dec 2023
Cited by 1 | Viewed by 1597
Abstract
The SARS-CoV-2 pandemic continues to pose a global threat. While its virulence has subsided, it has persisted due to the continual emergence of new mutations. Although many high-risk conditions related to COVID-19 have been identified, the understanding of protective factors remains limited. Intriguingly, [...] Read more.
The SARS-CoV-2 pandemic continues to pose a global threat. While its virulence has subsided, it has persisted due to the continual emergence of new mutations. Although many high-risk conditions related to COVID-19 have been identified, the understanding of protective factors remains limited. Intriguingly, epidemiological evidence suggests a low incidence of COVID-19-infected CD patients. The present study explores whether their genetic background, namely, the associated HLA-DQs, offers protection against severe COVID-19 outcomes. We hypothesize that the HLA-DQ2/8 alleles may shield CD patients from SARS-CoV-2 and its subsequent effects, possibly due to memory CD4 T cells primed by previous exposure to human-associated common cold coronaviruses (CCC) and higher affinity to those allele’s groove. In this context, we examined potential cross-reactivity between SARS-CoV-2 epitopes and human-associated CCC and assessed the binding affinity (BA) of these epitopes to HLA-DQ2/8. Using computational methods, we analyzed sequence similarity between SARS-CoV-2 and four distinct CCC. Of 924 unique immunodominant 15-mer epitopes with at least 67% identity, 37 exhibited significant BA to HLA-DQ2/8, suggesting a protective effect. We present various mechanisms that might explain the protective role of HLA-DQ2/8 in COVID-19-afflicted CD patients. If substantiated, these insights could enhance our understanding of the gene–environment enigma and viral–host relationship, guiding potential therapeutic innovations against the ongoing SARS-CoV-2 pandemic. Full article
(This article belongs to the Section Virology)
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